FMO DATABASE

FMODB ID: 3JNLL

Calculation Name: 4CZD-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4CZD

Chain ID: B

ChEMBL ID:

UniProt ID: B8J364

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	159
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1333988.912252
FMO2-HF: Nuclear repulsion	1270265.952435
FMO2-HF: Total energy	-63722.959817
FMO2-MP2: Total energy	-63905.6777

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET)

Summations of interaction energy for fragment #1(B:1:MET)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-16.161	-10.141	14.831	-6.402	-14.452	-0.018

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.004

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	B	3	HIS	0	0.005	0.002	3.697	-2.413	-0.338	-0.009	-0.926	-1.141	0.000
4	B	4	GLN	0	-0.092	-0.042	2.408	-2.355	-4.633	7.466	-2.140	-3.049	0.007
5	B	5	PHE	0	0.008	0.004	2.426	-1.449	0.102	1.504	-0.602	-2.453	0.000
6	B	6	SER	0	0.029	-0.013	4.908	-0.831	-0.861	-0.001	-0.009	0.040	0.000
7	B	7	PRO	0	0.003	-0.013	6.391	-0.331	-0.331	0.000	0.000	0.000	0.000
8	B	8	GLU	-1	-0.776	-0.857	8.145	-0.506	-0.506	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.742	-0.868	6.893	0.172	0.172	0.000	0.000	0.000	0.000
10	B	10	GLN	0	-0.058	-0.050	2.936	-1.301	-0.572	0.127	-0.191	-0.666	0.000
11	B	11	ALA	0	-0.040	0.002	5.734	-0.279	-0.279	0.000	0.000	0.000	0.000
12	B	12	VAL	0	0.068	0.033	9.424	-0.010	-0.010	0.000	0.000	0.000	0.000
13	B	13	LEU	0	-0.042	-0.019	5.261	-0.017	-0.017	0.000	0.000	0.000	0.000
14	B	14	ARG	1	0.835	0.910	5.412	1.773	1.773	0.000	0.000	0.000	0.000
15	B	15	ILE	0	0.006	0.030	8.135	0.057	0.057	0.000	0.000	0.000	0.000
16	B	16	VAL	0	0.025	-0.002	9.428	0.042	0.042	0.000	0.000	0.000	0.000
17	B	17	GLN	0	-0.111	-0.050	6.599	-0.376	-0.376	0.000	0.000	0.000	0.000
18	B	18	ALA	0	-0.072	-0.030	9.378	0.040	0.040	0.000	0.000	0.000	0.000
19	B	19	ASN	0	-0.053	-0.053	12.835	0.137	0.137	0.000	0.000	0.000	0.000
20	B	20	LEU	0	-0.006	0.017	15.033	-0.042	-0.042	0.000	0.000	0.000	0.000
21	B	21	PRO	0	0.005	0.000	16.844	0.003	0.003	0.000	0.000	0.000	0.000
22	B	22	ASP	-1	-0.948	-0.965	19.879	-0.229	-0.229	0.000	0.000	0.000	0.000
23	B	23	SER	0	-0.027	-0.052	23.234	0.022	0.022	0.000	0.000	0.000	0.000
24	B	24	LEU	0	-0.031	-0.023	24.781	0.001	0.001	0.000	0.000	0.000	0.000
25	B	25	THR	0	-0.030	-0.017	24.487	0.019	0.019	0.000	0.000	0.000	0.000
26	B	26	PRO	0	0.006	0.014	19.410	-0.008	-0.008	0.000	0.000	0.000	0.000
27	B	27	TYR	0	0.001	-0.020	16.714	-0.044	-0.044	0.000	0.000	0.000	0.000
28	B	28	ALA	0	0.051	0.022	18.474	-0.011	-0.011	0.000	0.000	0.000	0.000
29	B	29	ASP	-1	-0.788	-0.845	20.191	-0.259	-0.259	0.000	0.000	0.000	0.000
30	B	30	LEU	0	-0.016	-0.027	13.715	-0.036	-0.036	0.000	0.000	0.000	0.000
31	B	31	ALA	0	-0.038	-0.014	15.575	-0.038	-0.038	0.000	0.000	0.000	0.000
32	B	32	GLU	-1	-0.944	-0.966	16.983	-0.248	-0.248	0.000	0.000	0.000	0.000
33	B	33	GLN	0	-0.046	-0.024	15.879	-0.025	-0.025	0.000	0.000	0.000	0.000
34	B	34	ALA	0	-0.062	-0.023	12.200	-0.063	-0.063	0.000	0.000	0.000	0.000
35	B	35	GLY	0	-0.010	0.004	13.238	-0.018	-0.018	0.000	0.000	0.000	0.000
36	B	36	MET	0	-0.086	-0.045	11.199	0.032	0.032	0.000	0.000	0.000	0.000
37	B	37	THR	0	0.022	-0.006	16.460	0.008	0.008	0.000	0.000	0.000	0.000
38	B	38	GLU	-1	-0.815	-0.942	17.811	-0.158	-0.158	0.000	0.000	0.000	0.000
39	B	39	ALA	0	0.001	-0.003	18.722	0.000	0.000	0.000	0.000	0.000	0.000
40	B	40	GLN	0	0.047	0.039	14.782	0.001	0.001	0.000	0.000	0.000	0.000
41	B	41	VAL	0	0.035	0.032	13.989	0.018	0.018	0.000	0.000	0.000	0.000
42	B	42	LEU	0	-0.021	-0.013	14.777	0.007	0.007	0.000	0.000	0.000	0.000
43	B	43	GLU	-1	-0.832	-0.871	14.336	0.204	0.204	0.000	0.000	0.000	0.000
44	B	44	LEU	0	0.005	0.018	8.418	0.052	0.052	0.000	0.000	0.000	0.000
45	B	45	LEU	0	-0.017	-0.013	11.155	0.061	0.061	0.000	0.000	0.000	0.000
46	B	46	GLY	0	-0.018	-0.010	13.245	0.012	0.012	0.000	0.000	0.000	0.000
47	B	47	ARG	1	0.750	0.815	9.672	-0.336	-0.336	0.000	0.000	0.000	0.000
48	B	48	LEU	0	0.024	0.012	7.623	0.081	0.081	0.000	0.000	0.000	0.000
49	B	49	LYS	1	0.858	0.937	10.949	-0.005	-0.005	0.000	0.000	0.000	0.000
50	B	50	ALA	0	-0.038	-0.011	13.575	-0.033	-0.033	0.000	0.000	0.000	0.000
51	B	51	SER	0	0.011	0.002	10.082	-0.034	-0.034	0.000	0.000	0.000	0.000
52	B	52	GLY	0	-0.002	0.006	12.167	0.041	0.041	0.000	0.000	0.000	0.000
53	B	53	ALA	0	-0.046	-0.020	6.762	-0.071	-0.071	0.000	0.000	0.000	0.000
54	B	54	ILE	0	-0.023	0.001	7.705	-0.263	-0.263	0.000	0.000	0.000	0.000
55	B	55	ARG	1	0.970	0.974	10.253	0.382	0.382	0.000	0.000	0.000	0.000
56	B	56	ARG	1	0.864	0.913	12.653	0.280	0.280	0.000	0.000	0.000	0.000
57	B	57	PHE	0	0.063	0.034	12.208	-0.047	-0.047	0.000	0.000	0.000	0.000
58	B	58	GLY	0	0.038	0.019	15.330	0.048	0.048	0.000	0.000	0.000	0.000
59	B	59	ALA	0	0.030	0.030	17.342	-0.039	-0.039	0.000	0.000	0.000	0.000
60	B	60	SER	0	0.010	0.001	16.733	0.022	0.022	0.000	0.000	0.000	0.000
61	B	61	ILE	0	0.011	0.012	19.843	0.001	0.001	0.000	0.000	0.000	0.000
62	B	62	LYS	1	0.957	0.970	23.054	0.235	0.235	0.000	0.000	0.000	0.000
63	B	63	HIS	0	0.013	0.005	24.449	0.011	0.011	0.000	0.000	0.000	0.000
64	B	64	GLN	0	0.058	0.021	24.765	0.005	0.005	0.000	0.000	0.000	0.000
65	B	65	LYS	1	0.888	0.948	27.513	0.101	0.101	0.000	0.000	0.000	0.000
66	B	66	THR	0	0.037	0.025	27.472	0.010	0.010	0.000	0.000	0.000	0.000
67	B	67	GLY	0	0.030	0.018	30.438	-0.005	-0.005	0.000	0.000	0.000	0.000
68	B	68	DTR	0	-0.034	-0.014	27.720	-0.015	-0.015	0.000	0.000	0.000	0.000
69	B	69	THR	0	-0.036	-0.011	30.640	0.010	0.010	0.000	0.000	0.000	0.000
70	B	70	HIS	0	0.074	0.024	30.906	-0.010	-0.010	0.000	0.000	0.000	0.000
71	B	71	ASN	0	-0.027	-0.028	26.809	-0.008	-0.008	0.000	0.000	0.000	0.000
72	B	72	ALA	0	0.016	0.014	29.743	0.000	0.000	0.000	0.000	0.000	0.000
73	B	73	MET	0	0.015	0.027	24.254	-0.002	-0.002	0.000	0.000	0.000	0.000
74	B	74	VAL	0	-0.016	-0.010	28.288	0.003	0.003	0.000	0.000	0.000	0.000
75	B	75	ALA	0	0.007	0.022	28.812	0.000	0.000	0.000	0.000	0.000	0.000
76	B	76	TRP	0	0.015	-0.025	30.214	0.001	0.001	0.000	0.000	0.000	0.000
77	B	77	LYS	1	0.828	0.902	31.678	-0.007	-0.007	0.000	0.000	0.000	0.000
78	B	78	VAL	0	-0.043	-0.020	30.353	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	79	THR	0	0.008	-0.011	33.714	0.002	0.002	0.000	0.000	0.000	0.000
80	B	80	PRO	0	0.025	-0.013	31.737	-0.001	-0.001	0.000	0.000	0.000	0.000
81	B	81	ASP	-1	-0.858	-0.905	32.302	0.047	0.047	0.000	0.000	0.000	0.000
82	B	82	GLN	0	-0.006	-0.015	34.358	-0.002	-0.002	0.000	0.000	0.000	0.000
83	B	83	VAL	0	-0.026	0.003	27.658	-0.007	-0.007	0.000	0.000	0.000	0.000
84	B	84	ASP	-1	-0.864	-0.935	28.644	0.065	0.065	0.000	0.000	0.000	0.000
85	B	85	ASP	-1	-0.777	-0.871	29.912	0.016	0.016	0.000	0.000	0.000	0.000
86	B	86	CYS	0	-0.021	-0.009	32.623	-0.007	-0.007	0.000	0.000	0.000	0.000
87	B	87	GLY	0	0.023	0.009	28.371	-0.008	-0.008	0.000	0.000	0.000	0.000
88	B	88	ARG	1	0.862	0.927	28.760	-0.035	-0.035	0.000	0.000	0.000	0.000
89	B	89	LYS	1	0.810	0.884	29.835	-0.022	-0.022	0.000	0.000	0.000	0.000
90	B	90	ALA	0	-0.011	-0.003	29.930	-0.006	-0.006	0.000	0.000	0.000	0.000
91	B	91	ALA	0	-0.048	-0.031	26.884	-0.009	-0.009	0.000	0.000	0.000	0.000
92	B	92	GLU	-1	-0.916	-0.951	28.635	-0.005	-0.005	0.000	0.000	0.000	0.000
93	B	93	HIS	0	-0.066	-0.035	31.280	-0.008	-0.008	0.000	0.000	0.000	0.000
94	B	94	SER	0	0.014	-0.008	30.751	-0.004	-0.004	0.000	0.000	0.000	0.000
95	B	95	HIS	0	-0.064	-0.022	31.199	-0.007	-0.007	0.000	0.000	0.000	0.000
96	B	96	ILE	0	-0.029	-0.012	27.192	-0.009	-0.009	0.000	0.000	0.000	0.000
97	B	97	SER	0	-0.012	-0.003	23.247	-0.002	-0.002	0.000	0.000	0.000	0.000
98	B	98	HIS	0	-0.035	-0.003	18.634	0.003	0.003	0.000	0.000	0.000	0.000
99	B	99	VAL	0	0.045	0.024	23.130	0.001	0.001	0.000	0.000	0.000	0.000
100	B	100	TYR	0	-0.068	-0.052	18.343	-0.004	-0.004	0.000	0.000	0.000	0.000
101	B	101	TYR	0	0.013	-0.014	23.256	-0.002	-0.002	0.000	0.000	0.000	0.000
102	B	102	ARG	1	0.829	0.906	17.850	0.060	0.060	0.000	0.000	0.000	0.000
103	B	103	PRO	0	0.032	0.014	23.400	-0.010	-0.010	0.000	0.000	0.000	0.000
104	B	104	SER	0	-0.050	-0.040	25.241	-0.002	-0.002	0.000	0.000	0.000	0.000
105	B	105	SER	0	-0.004	0.000	27.869	-0.003	-0.003	0.000	0.000	0.000	0.000
106	B	106	ALA	0	0.000	0.012	29.318	0.001	0.001	0.000	0.000	0.000	0.000
107	B	107	PRO	0	-0.005	-0.014	31.082	-0.004	-0.004	0.000	0.000	0.000	0.000
108	B	108	ASP	-1	-0.922	-0.955	33.134	0.001	0.001	0.000	0.000	0.000	0.000
109	B	109	TRP	0	-0.042	-0.032	27.799	-0.012	-0.012	0.000	0.000	0.000	0.000
110	B	110	PRO	0	0.042	0.034	30.901	0.004	0.004	0.000	0.000	0.000	0.000
111	B	111	TYR	0	-0.041	-0.016	30.408	0.002	0.002	0.000	0.000	0.000	0.000
112	B	112	GLU	-1	-0.741	-0.841	27.700	0.052	0.052	0.000	0.000	0.000	0.000
113	B	113	MET	0	-0.003	0.018	26.829	0.000	0.000	0.000	0.000	0.000	0.000
114	B	114	TYR	0	-0.061	-0.025	24.825	-0.015	-0.015	0.000	0.000	0.000	0.000
115	B	115	THR	0	0.045	0.026	26.195	0.004	0.004	0.000	0.000	0.000	0.000
116	B	116	MET	0	-0.074	-0.040	24.341	-0.005	-0.005	0.000	0.000	0.000	0.000
117	B	117	ILE	0	0.049	0.039	26.874	-0.003	-0.003	0.000	0.000	0.000	0.000
118	B	118	HIS	1	0.821	0.891	25.561	0.109	0.109	0.000	0.000	0.000	0.000
119	B	119	GLY	0	0.068	0.032	30.754	0.009	0.009	0.000	0.000	0.000	0.000
120	B	120	ARG	1	0.821	0.886	33.793	0.057	0.057	0.000	0.000	0.000	0.000
121	B	121	SER	0	0.007	-0.018	36.617	0.001	0.001	0.000	0.000	0.000	0.000
122	B	122	GLU	-1	-0.798	-0.889	36.741	-0.067	-0.067	0.000	0.000	0.000	0.000
123	B	123	ALA	0	0.042	0.021	38.306	0.002	0.002	0.000	0.000	0.000	0.000
124	B	124	GLU	-1	-0.775	-0.848	36.783	-0.063	-0.063	0.000	0.000	0.000	0.000
125	B	125	CYS	0	-0.022	-0.009	34.211	0.000	0.000	0.000	0.000	0.000	0.000
126	B	126	LEU	0	0.021	-0.007	35.876	0.003	0.003	0.000	0.000	0.000	0.000
127	B	127	GLY	0	0.029	0.016	38.376	0.004	0.004	0.000	0.000	0.000	0.000
128	B	128	VAL	0	0.005	0.002	33.367	0.004	0.004	0.000	0.000	0.000	0.000
129	B	129	VAL	0	-0.005	0.007	34.782	0.004	0.004	0.000	0.000	0.000	0.000
130	B	130	GLU	-1	-0.797	-0.885	36.712	-0.019	-0.019	0.000	0.000	0.000	0.000
131	B	131	ASP	-1	-0.802	-0.872	37.459	-0.024	-0.024	0.000	0.000	0.000	0.000
132	B	132	VAL	0	0.018	0.026	33.403	0.004	0.004	0.000	0.000	0.000	0.000
133	B	133	LYS	1	0.784	0.876	36.582	0.025	0.025	0.000	0.000	0.000	0.000
134	B	134	ARG	1	0.811	0.906	39.460	0.023	0.023	0.000	0.000	0.000	0.000
135	B	135	THR	0	-0.056	-0.043	37.389	0.002	0.002	0.000	0.000	0.000	0.000
136	B	136	THR	0	-0.048	-0.025	34.261	0.005	0.005	0.000	0.000	0.000	0.000
137	B	137	SER	0	0.024	0.015	37.375	-0.001	-0.001	0.000	0.000	0.000	0.000
138	B	138	LEU	0	0.024	0.020	32.440	0.002	0.002	0.000	0.000	0.000	0.000
139	B	139	LYS	1	0.956	0.965	36.918	-0.006	-0.006	0.000	0.000	0.000	0.000
140	B	140	GLU	-1	-0.817	-0.882	38.084	0.002	0.002	0.000	0.000	0.000	0.000
141	B	141	HIS	0	-0.041	-0.037	34.584	-0.002	-0.002	0.000	0.000	0.000	0.000
142	B	142	ALA	0	0.042	0.026	32.710	0.000	0.000	0.000	0.000	0.000	0.000
143	B	143	ILE	0	-0.011	-0.010	32.267	-0.004	-0.004	0.000	0.000	0.000	0.000
144	B	144	LEU	0	-0.023	-0.006	27.552	-0.001	-0.001	0.000	0.000	0.000	0.000
145	B	145	ARG	1	0.898	0.928	29.501	0.051	0.051	0.000	0.000	0.000	0.000
146	B	146	SER	0	0.013	0.002	27.684	0.000	0.000	0.000	0.000	0.000	0.000
147	B	147	LEU	0	0.004	0.007	29.501	-0.005	-0.005	0.000	0.000	0.000	0.000
148	B	148	LYS	1	0.951	0.962	28.865	0.153	0.153	0.000	0.000	0.000	0.000
149	B	149	GLU	-1	-0.835	-0.875	23.709	-0.253	-0.253	0.000	0.000	0.000	0.000
150	B	150	LEU	0	0.008	-0.004	24.149	0.000	0.000	0.000	0.000	0.000	0.000
151	B	151	LYS	1	0.966	0.976	16.244	0.448	0.448	0.000	0.000	0.000	0.000
152	B	152	LYS	1	0.849	0.911	18.938	0.278	0.278	0.000	0.000	0.000	0.000
153	B	153	THR	0	-0.018	-0.016	14.265	-0.030	-0.030	0.000	0.000	0.000	0.000
154	B	154	SER	0	0.018	0.013	12.247	0.084	0.084	0.000	0.000	0.000	0.000
155	B	155	MET	0	-0.029	-0.009	5.583	0.147	0.147	0.000	0.000	0.000	0.000
156	B	156	THR	0	0.011	0.010	7.575	0.037	0.037	0.000	0.000	0.000	0.000
157	B	157	TYR	0	-0.009	-0.014	2.574	-0.406	0.356	0.337	-0.208	-0.891	0.001
158	B	158	PHE	0	0.042	0.028	2.423	-9.793	-6.784	5.406	-2.307	-6.108	-0.026
159	B	159	THR	0	0.035	0.030	4.026	1.027	1.229	0.001	-0.019	-0.184	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET)